Dexter
believes that young psychopath Zach Hamilton is about to kill a
waitress, named Sofia, who works at his father's yacht club.

So Dexter heads down to the yacht club to head him off, and spots Zach waiting outside in a parked car.

Meanwhile,
Dex sees Quinn, who is also following Zach. ( To get Quinn out of
the way, Dexter phones Jamie and tells her she should invite Quinn
over. That works. )

Dexter sees
Sofia walk up a gangway, and then sees that Zach's father is with
her. The two kiss, and Dexter realizes Mr. Hamilton is cheating
on his wife again (his previous affair was with the murdered Norma Rivera).

Dex sees Zach get out of his car, carrying a large knife, and moves to intercept him.

But instead
of trying to kill Norma, Zach instead is about to kill his father, when
Dex suddenly appears and knocks Zach out with his needle.

Just then,
Quinn pulls up in a car, and tells Dexter that he knows what he is
doing. But Quinn only thinks that Dex is playing detective and following
Zach.

Later, when
he has Zach on his table, Dexter learns that Zach is killing to protect
his mother, and takes Dr. Vogel's advice to become a mentor to Zach,
rather than killing him.

Q. What is it actually in real life?

A. A building at a marina, a smaller building nearby,
a marina gangway, and the surrounding parking lot.

Q. Where can I find it in real life?

A. This building and parking lot are part of the Cabrillo Marina complex, in San Pedro, CA.

That complex is composed of
multiple buildings, clustered around the large marina, many of them
almost identical to one another: white, Spanish-style buildings with
red-tile roofs.

The irony is that there actually is a yacht club at this marina, as well
as restaurants, but they
didn't use that actual yacht club building for the scene.

Instead, the building that you see, when Dex first arrives in his car - the one with the sign reading "Bay Terrace", where Quinn is waiting - is located at the east end of a street called Whalers Walk (which is more like a road inside of a parking lot).

To reach the building from the Cabrillo Plaza fountain (where they filmed the earlier bloody crime scene),
you drive past the fountain and turn right (east) into the
parking lot on Whalers Walk. Drive east to the very end of Whalers
Walk, and it's the big, two-story building in front of you to your left. A
large sign outside says 210 - Berth 31, and lists a number of yacht dealers.

They changed that sign to read "Bay Terrace" for the scene, used some color flood lights on the walls, and added a name banner to the second floor balcony.

There are several different locations in this scene - clustered in the same area: The restaurant building, the spot where Zach parks, the marina gangway
where Zach's father enters with Sofia, the building Mr.
Hamilton walks past when Zach was stalking him, and the spot where Dexter
captures Zach with his hypodermic. (You can see the exact locations on this aerial photo map.)

I shot the photos below in August 2013.

The first location is the yacht club / restaurant building: (The camera here is looking northeast)

The second is the marina gate(29-C) where Mr. Hamilton & Sophia walk up a gangway, then kiss.
It's the farthest gate to the east, on the south edge of the marina complex:

(The camera here is looking southeast)

The third location is the small, low building that Mr. Hamilton walks past, while Zach is stalking him.
It is just west of that gate 29-C. He was walking west as Zach stalked him:

(The camera here is looking east.)

And the fourth is the corner where Dexter captures Zach, moments before he would have killed his father.
Dexter sprang out from the building's southeast corner, that you see marked by the red X.

(In this photo, the camera here is looking south, towards the marina slips.)

A. They filmed the earlier crime scene
(with Zach) here at the Cabrillo Marina, so it was obvious that this
night scene was also shot somewhere in that same marina complex.
The only problem was pinpointing which buildings they used, since many
of them tend to look alike.

Fortunately, this particular
building (the one used as the yacht club restaurant) has a unique
flower-shaped keyhole window on its west side, which is visible as
Dexter drives past the yacht club at the start of the scene.

So it was just a matter of using aerial photos to look at the various buildings until I found the one with the window
that matched. There is no Google StreetView on Whalers Walk, but
fortunately there is Bing's StreetSide View, and that allowed me to get a
great look at the building. And then I drove down there to verify
it, and to shoot the photos you see above.